It is still not known what causes anencephaly. It is probably triggered by a combination of genetic and environmental factors (Sadler 2005). We nevertheless know that taking Folic Acid can prevent anencephaly. Some medicines (the pill, valproic acid, antimetabolic drugs and others) lower Folic Acid levels, hence taking them increases the risk of giving birth to a child with anencephaly (Sadler, 2005).
Ninety-five percent of infants with anencephaly are born in families with no history of neural-tube defect. Once an infant with anencephaly has been born, the risk increases to 2 to 5 percent in subsequent pregnancies (Stumpf 1990)
Chromosomal abnormalities, single-gene mutations, and teratogenic causes are indentified in fewer than 10 percent of affected infants (Holmes 1976)
(Source: http://www.anencephaly.info/e/faq.php#8 )